With the increasing penetration of new energy such as wind turbine(WT) and photovoltaic(PV) output in the energy system, the consumption of new energy in the energy system has become an urgent problem to be solved. At the same time, shared energy storage continues to participate in the grid connection, and the trading relationship between shared energy storage and other participants in the energy system is also the key to the optimization of power scheduling in the energy system. In this context, taking the energy system with micro-grids(MGs) and shared energy storage (SES) as the research object, and considering the uncertainty of new energy output, the energy system scheduling mechanism was designed based on Stackelberg game. The results of example analysis show that the actual energy capacity and power capacity of SESC have decreased by 11.83% and 31.89% respectively, and the new energy consumption rates of MGS has increased to more than 90%. The Stackelberg game scheduling strategy improves the overall operating income and stability of the energy system.